Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska

Abstract

The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.

Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

“…Our results therefore demonstrate that straying and subsequent gene flow from hatchery releases have reduced the genetic divergence among remaining wild Atlantic salmon populations in the Gulf of Finland. Similar alterations of genetic structure due to unidirectional gene flow from reared conspecifics as a result of straying (Vasem€ agi et al 2005a;Jasper et al 2013), direct stocking (Hansen 2002;Eldridge et al 2009;Lamaze et al 2012;Marie et al 2010;Perrier et al 2013) or farm escapes (Skaala et al 2006;Bourret et al 2011;Glover et al 2012) have also been observed in earlier studies on Atlantic salmon and other salmonids.…”

“…; Jasper et al . ). However, it is not always the case, as hatchery fish may carry unique alleles not observed in wild populations (Verspoor ); thus, hatchery releases may also increase the genetic variability of wild populations, particularly if the source populations for hatchery stocks are larger than the wild populations.…”

“…Both microsatellite and SNP markers revealed congruent temporal patterns, suggesting that introgression has changed the genetic make-up of wild populations by reducing genetic divergence and increasing genetic diversity. The increase in genetic diversity as a result of unidirectional gene flow from hatchery releases contradicts the typical perception that farmed strains often possess reduced genetic diversity relative to wild popu- lations (Ryman & Laikre 1991;Blanchet et al 2008;Hutchings & Fraser 2008;Araki & Schmid 2010); thus, the introgression of reared fish is expected to reduce the genetic variability of wild populations (Eldridge et al 2009;Bourret et al 2011;Jasper et al 2013). However, it is not always the case, as hatchery fish may carry unique alleles not observed in wild populations (Verspoor 1998); thus, hatchery releases may also increase the genetic variability of wild populations, particularly if the source populations for hatchery stocks are larger than the wild populations.…”

“…; Jasper et al . ; Hohenlohe et al . ), which makes the accurate characterization of introgressive hybridization a challenging task.…”

“…Because of the potential negative effects of introgressive hybridization, a large number of studies have evaluated both the short-and long-term genetic consequences of stocking in salmonid fishes (Vasem€ agi et al 2005a;Hansen et al , 2010Lamaze et al 2012;Perrier et al 2013). However, most of these studies relied on a relatively small number of genetic markers (tens of loci, but see Lamaze et al 2012;Jasper et al 2013;Hohenlohe et al 2013), which makes the accurate characterization of introgressive hybridization a challenging task. Thus, the uncertainty of hybrid identification increases when the hybridizing populations are closely related and it is not possible to utilize diagnostic alleles.…”